Author

Yan Jia

Chinese Academy of Sciences

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Biology Disciplines

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Bioinformatics· 2 Genomics· 2

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Research Focus:gene regulatory network inference· 4 Organism:human· 4 Approach:statistical model· 4 Assay:ATAC-seq· 2 Assay:Hi-C· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Assay:ChIP-seq· 1

Frequent Co-Authors

Bingxiang XuiD· 4 shared Zhihua ZhangiD· 4 shared Feifei LiiD· 2 shared Xiaoli Li· 2 shared Danyang WangiD· 1 shared Feifei LiiD· 1 shared Feifei Li· 1 shared Hui Zhang· 1 shared

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2016-2022 · peak 1/yr

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10 top collaborators · 30 mutual co-author links

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4 shared papersGenomics

Bingxiang XuORCID

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4 papers

Recent·Most cited

Cell cycle arrest explained the observed bulk 3D genomic alterations in response to long term heat shock for mammalian cells

Bingxiang Xu, Xiaomeng Gao, Xiaoli Li, Yan Jia, Feifei Li, Zhihua Zhang

The paper shows that long-term heat shock causes chromatin conformation changes in K562 cells due to cell cycle arrest, not chromatin accessibility changes.

Genome Research · Jul 1, 2022Peer-reviewedGenomics

Decoding nucleosome positions with ATAC-seq data at single-cell level

Bingxiang Xu, Xiaoli Li, Xiaomeng Gao, Yan Jia, Feifei Li, Zhihua Zhang

The paper introduces deNOPA, a tool for predicting nucleosome positions from ATAC-seq data, showing it outperforms existing tools and works with ultrasparse data.

bioRxiv · Feb 7, 2021 · PreprintBioinformatics

Widespread transcriptional responses to the thermal stresses are prewired in human 3D genome

Xiaoli Li, Bingxiang Xu, Xiao Li, Danyang Wang, Ziyang An, Yan Jia, Jing Niu, Juntao Tony Gao, Michael Q. Zhang, Feifei Li, Zhihua Zhang

The paper shows that transcriptional responses to thermal stress in human cells are prewired in the 3D genome, with chromatin and epigenetic settings playing a key role.

bioRxiv · Aug 7, 2019 · PreprintGenomics

Characteristic arrangement of nucleosomes is predictive of chromatin interactions at kilobase resolution

Hui Zhang, Feifei Li, Yan Jia, Bingxiang Xu, Yiqun Zhang, Xiaoli Li, Zhihua Zhang

The paper introduces CISD and CISD_loop methods to predict chromatin interactions from MNase-seq and Hi-C data, achieving kilobase resolution with low data requirements.

bioRxiv · Jul 31, 2016Bioinformatics